Couple thoughts. In the old 2e Forgotten Realms box set about Netheril, there are a number of level 9+ spells. One of them was “Proctiv’s Breach Crystal Sphere,” an 11th-level spell. The reverse of this spell would permanently LOCK a crystal sphere, making it impassable. Granted, planar travel to and from was still a possibility. But I always felt that something similar could explain why Athas is so cut off and isolated (and directly and simply explains why Athas’ crystal sphere is impassable).
But I don’t think it’s due to Rajaat. The planar experiments to the south that created the deadlands make it pretty clear that planar travel / plane walking were NOT really in Rajaat’s wheelhouse of skills. He didn’t know how it worked, really. Which is why those experiments were ongoing for centuries, and ultimately wound up in the gate experiment that killed everyone.
However, Dregoth’s planar mirror make it clear and obvious that SOMEONE knew about and participated in planar travel, before ultimately being lost and forgotten in time. Whoever that someone was, maybe THEY had something to di with (or at least better understood) the isolated planar nature of Athas and its sealed crystal sphere.
Another thing to consider is the Githyanki city of Yathazor and the history of the gith. It’s never clearly stated how long ago that all went down. So maybe the original githyanki incursion predated the isolation. Maybe the githzerai mind bomb that devolved all the githynki into the gith was related to the isolation.
Things to consider.